Ava Amini

Principal Researcher

论文与出版物

查看方式：

- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Causal integration of chemical structures improves representations of microscopy images for morphological profiling
  
  Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
  
  April 2025
  
  DOI Publication Publication Github
- Toward deep learning sequence–structure co-generation for protein design
  
  Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
  
  Current Opinion in Structural Biology | March 2025
  
  DOI Publication
- Deep learning guided design of protease substrates
  
  Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
  
  bioRxiv | March 2025
  
  DOI
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI 项目
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 第 21 卷
  
  DOI Publication
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint 项目
- Deeper evaluation of a single-cell foundation model
  
  Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
  
  Nature Machine Intelligence | December 2024
  
  DOI Publication
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Access
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- Scalable, compressed phenotypic screening using pooled perturbations.
  
  Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
  
  Nature biotechnology | October 2024
  
  DOI Publication 项目
- Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
  
  Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
  
  bioRxiv | June 2024
  
  Preprint 项目
- A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
  
  Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | March 2024
  
  Preprint 项目
- Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
  
  Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
  
  ICML 2024 | February 2024
  
  DOI Publication
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint 项目
- Protein structure generation via folding diffusion
  
  Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
  
  Nature Communications | February 2024, 第 15 卷
  
  DOI PDF Publication
- Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
  
  Science | January 2024, 第 383 卷: pp. eadf2341-eadf2341
  
  DOI Publication
- Assessing the limits of zero-shot foundation models in single-cell biology
  
  Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
  
  bioRxiv | November 2023
  
  Preprint PDF 项目
- Continuous Time Evidential Distributions for Irregular Time Series
  
  Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
  
  ArXiv | July 2023
  
  DOI Preprint
- Deep self-supervised learning for biosynthetic gene cluster detection and product classification
  
  Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
  
  PLOS Computational Biology | May 2023, 第 19 卷(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 第 3 卷: pp. 366-367
  
  DOI Publication
- Low protease activity in B cell follicles promotes retention of intact antigens after immunization
  
  Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
  
  Science | January 2023, 第 379 卷(379): pp. eabn8934
  
  Publication
- A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
  
  bioRxiv | January 2023
  
  Preprint DOI
- Multiscale profiling of protease activity in cancer
  
  Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
  
  Nature Communications | October 2022, 第 13 卷(1)
  
  Publication
- Protease activity analysis: A toolkit for analyzing enzyme activity data
  
  Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
  
  ACS Omega | July 2022, 第 7 卷(28): pp. 24292-24301
  
  Publication
- Host protease activity classifies pneumonia etiology
  
  Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
  
  Proceedings of the National Academy of Sciences of the United States of America | June 2022, 第 19 卷(25)
  
  Publication
- Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
  
  Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
  
  Advanced Healthcare Materials | February 2022, 第 11 卷(11)
  
  Publication
- Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
  
  Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
  
  ACS Synthetic Biology | August 2021, 第 10 卷(9): pp. 2231-2242
  
  DOI Publication
- Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
  
  Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
  
  ACS Central Science | July 2021, 第 7 卷(8): pp. 1356-1367
  
  Publication
- Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
  
  Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
  
  Cancer Research | January 2021, 第 81 卷(1): pp. 213-224
  
  DOI
- Deep Evidential Regression
  
  Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
  
  2020 Neural Information Processing Systems | December 2020
  
  PDF Publication
- Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
  
  Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
  
  Nature Biomedical Engineering | May 2020, 第 4 卷(6): pp. 636-648
  
  DOI 项目
- Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
  
  Ava P. Soleimany, Sangeeta N. Bhatia
  
  Trends in Molecular Medicine | April 2020, 第 26 卷(5): pp. 450-468
  
  DOI
- Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
  
  Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
  
  Science Translational Medicine | March 2020, 第 12 卷(537)
  
  DOI
- Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
  
  Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
  
  Nature Nanotechnology | August 2019, 第 14 卷(9): pp. 883-890
  
  DOI
- Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
  
  Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
  
  AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019
  
  DOI
- Synthetic recombinase-based state machines in living cells
  
  Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
  
  Science | July 2016, 第 353 卷(6297): pp. 363-363
  
  DOI

- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Causal integration of chemical structures improves representations of microscopy images for morphological profiling
  
  Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
  
  April 2025
  
  DOI Publication Publication Github
- Toward deep learning sequence–structure co-generation for protein design
  
  Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
  
  Current Opinion in Structural Biology | March 2025
  
  DOI Publication
- Deep learning guided design of protease substrates
  
  Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
  
  bioRxiv | March 2025
  
  DOI
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI 项目
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 第 21 卷
  
  DOI Publication
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint 项目
- Deeper evaluation of a single-cell foundation model
  
  Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
  
  Nature Machine Intelligence | December 2024
  
  DOI Publication
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Access
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- Scalable, compressed phenotypic screening using pooled perturbations.
  
  Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
  
  Nature biotechnology | October 2024
  
  DOI Publication 项目
- Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
  
  Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
  
  bioRxiv | June 2024
  
  Preprint 项目
- A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
  
  Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | March 2024
  
  Preprint 项目
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint 项目
- Protein structure generation via folding diffusion
  
  Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
  
  Nature Communications | February 2024, 第 15 卷
  
  DOI PDF Publication
- Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
  
  Science | January 2024, 第 383 卷: pp. eadf2341-eadf2341
  
  DOI Publication
- Deep self-supervised learning for biosynthetic gene cluster detection and product classification
  
  Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
  
  PLOS Computational Biology | May 2023, 第 19 卷(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 第 3 卷: pp. 366-367
  
  DOI Publication
- Low protease activity in B cell follicles promotes retention of intact antigens after immunization
  
  Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
  
  Science | January 2023, 第 379 卷(379): pp. eabn8934
  
  Publication
- A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
  
  bioRxiv | January 2023
  
  Preprint DOI
- Multiscale profiling of protease activity in cancer
  
  Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
  
  Nature Communications | October 2022, 第 13 卷(1)
  
  Publication
- Protease activity analysis: A toolkit for analyzing enzyme activity data
  
  Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
  
  ACS Omega | July 2022, 第 7 卷(28): pp. 24292-24301
  
  Publication
- Host protease activity classifies pneumonia etiology
  
  Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
  
  Proceedings of the National Academy of Sciences of the United States of America | June 2022, 第 19 卷(25)
  
  Publication
- Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
  
  Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
  
  Advanced Healthcare Materials | February 2022, 第 11 卷(11)
  
  Publication
- Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
  
  Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
  
  ACS Synthetic Biology | August 2021, 第 10 卷(9): pp. 2231-2242
  
  DOI Publication
- Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
  
  Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
  
  Cancer Research | January 2021, 第 81 卷(1): pp. 213-224
  
  DOI
- Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
  
  Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
  
  Nature Biomedical Engineering | May 2020, 第 4 卷(6): pp. 636-648
  
  DOI 项目
- Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
  
  Ava P. Soleimany, Sangeeta N. Bhatia
  
  Trends in Molecular Medicine | April 2020, 第 26 卷(5): pp. 450-468
  
  DOI
- Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
  
  Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
  
  Science Translational Medicine | March 2020, 第 12 卷(537)
  
  DOI
- Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
  
  Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
  
  Nature Nanotechnology | August 2019, 第 14 卷(9): pp. 883-890
  
  DOI
- Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
  
  Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
  
  AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019
  
  DOI
- Synthetic recombinase-based state machines in living cells
  
  Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
  
  Science | July 2016, 第 353 卷(6297): pp. 363-363
  
  DOI
- Causal integration of chemical structures improves representations of microscopy images for morphological profiling
  
  Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
  
  April 2025
  
  DOI Publication Publication Github
- Toward deep learning sequence–structure co-generation for protein design
  
  Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
  
  Current Opinion in Structural Biology | March 2025
  
  DOI Publication
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 第 21 卷
  
  DOI Publication
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Access
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
  
  Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
  
  ICML 2024 | February 2024
  
  DOI Publication
- Protein structure generation via folding diffusion
  
  Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
  
  Nature Communications | February 2024, 第 15 卷
  
  DOI PDF Publication
- Assessing the limits of zero-shot foundation models in single-cell biology
  
  Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
  
  bioRxiv | November 2023
  
  Preprint PDF 项目
- Continuous Time Evidential Distributions for Irregular Time Series
  
  Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
  
  ArXiv | July 2023
  
  DOI Preprint
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 第 3 卷: pp. 366-367
  
  DOI Publication
- Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
  
  Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
  
  ACS Central Science | July 2021, 第 7 卷(8): pp. 1356-1367
  
  Publication
- Deep Evidential Regression
  
  Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
  
  2020 Neural Information Processing Systems | December 2020
  
  PDF Publication
- Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
  
  Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
  
  Science Translational Medicine | March 2020, 第 12 卷(537)
  
  DOI
- Synthetic recombinase-based state machines in living cells
  
  Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
  
  Science | July 2016, 第 353 卷(6297): pp. 363-363
  
  DOI

- scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling
  
  Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson, Aniket Tolpadi, Abhejit Rajagopal, Henry Miller, ashley conard, David Alvarez-Melis, Rory Stark, Simone Bianco, Morgan Levine, Ava P. Amini, Alex Lu, Nicolo Fusi, Ravi Pandya, Valentina Pedoia, Hana El-Samad
  
  NeurIPS 2025 | October 2025
  
  Publication
- Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models
  
  Francesca-Zhoufan Li, Ava P. Amini, Yisong Yue, Kevin Yang, Alex Lu
  
  ICML 2024 | February 2024
  
  DOI Publication
- Deep Evidential Regression
  
  Alexander Amini, Wilko Schwarting, Ava Soleimany, Daniela Rus
  
  2020 Neural Information Processing Systems | December 2020
  
  PDF Publication
- Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure
  
  Alexander Amini, Ava P. Soleimany, Wilko Schwarting, Sangeeta N. Bhatia, Daniela Rus
  
  AAAI/ACM Conference on Artificial Intelligence, Ethics, and Society | January 2019
  
  DOI
- Causal integration of chemical structures improves representations of microscopy images for morphological profiling
  
  Yemin Yu, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Lu
  
  April 2025
  
  DOI Publication Publication Github
- Toward deep learning sequence–structure co-generation for protein design
  
  Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang
  
  Current Opinion in Structural Biology | March 2025
  
  DOI Publication
- Deep learning guided design of protease substrates
  
  Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini
  
  bioRxiv | March 2025
  
  DOI
- Consequences of training data composition for deep learning models in single-cell biology
  
  Ajay Nadig, Akshaya Thoutam, Madeline Hughes, Anay Gupta, Andrew W. Navia, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2025
  
  Publication DOI 项目
- Benchmarking uncertainty quantification for protein engineering
  
  Kevin P. Greenman, Ava P. Amini, Kevin Kaichuang Yang
  
  PLOS Computational Biology | January 2025, 第 21 卷
  
  DOI Publication
- Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
  
  Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Nicolo Fusi, Andrew W. Navia, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | December 2024
  
  Preprint 项目
- Deeper evaluation of a single-cell foundation model
  
  Rebecca Boiarsky, Nalini M. Singh, Alejandro Buendia, Ava P. Amini, Gad Getz, David Sontag
  
  Nature Machine Intelligence | December 2024
  
  DOI Publication
- Protein generation with evolutionary diffusion: sequence is all you need
  
  Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M. Moses, Alex Lu, Nicolo Fusi, Ava P. Amini, Kevin Kaichuang Yang
  
  bioRxiv | November 2024
  
  DOI Preprint Access
- ProtNote: a multimodal method for protein-function annotation
  
  Samir Char, Nathaniel Corley, Sarah Alamdari, Kevin Kaichuang Yang, Ava P. Amini
  
  bioRxiv | October 2024
  
  DOI Preprint
- Scalable, compressed phenotypic screening using pooled perturbations.
  
  Nuo Liu, Walaa E. Kattan, Benjamin E. Mead, Conner Kummerlowe, Thomas Cheng, Sarah Ingabire, Jaime H Cheah, Christian K Soule, Anita Vrcic, Jane K. McIninch, Sergio Triana, Manuel Guzman, Tyler T. Dao, Joshua M. Peters, Kristen E. Lowder, Lorin Crawford, Ava P. Amini, Paul C. Blainey, William C. Hahn, Brian Cleary, Bryan D. Bryson, Peter S. Winter, Srivatsan Raghavan, Alex K. Shalek
  
  Nature biotechnology | October 2024
  
  DOI Publication 项目
- Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease
  
  Peter S. Winter, Michelle L. Ramseier, Andrew W. Navia, Sachit D. Saksena, Haley Strouf, Nezha Senhaji, Alan DenAdel, Mahnoor Mirza, Hyun Hwan An, Laura L. Bilal, Peter Dennis, Catharine S. Leahy, Kay Shigemori, Jennyfer Galves-Reyes, Ye Zhang, Foster Powers, Nolawit Mulugeta, Alejandro J. Gupta, Nicholas L. Calistri, Alexandria van Scoyk, Kristen Jones, Huiyun Liu, Kristen Stevenson, S. Ren, M. Luskin, Charles P. Couturier, Ava P. Amini, Srivatsan Raghavan, Robert J. Kimmerling, Mark M. Stevens, Lorin Crawford, David M. Weinstock, Scott R. Manalis, Alex K. Shalek, Mark A. Murakami
  
  bioRxiv | June 2024
  
  Preprint 项目
- A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
  
  Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | March 2024
  
  Preprint 项目
- Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
  
  Chibuikem Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolo Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford
  
  bioRxiv | February 2024
  
  Preprint 项目
- Protein structure generation via folding diffusion
  
  Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, Sarah Alamdari, James Zou, Alex Lu, Ava P. Amini
  
  Nature Communications | February 2024, 第 15 卷
  
  DOI PDF Publication
- Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sainetra Sridhar, Andjela Crnjac, Sahil Patel, Zhenyi An, Ahmet Bekdemir, Douglas Shea, Shih-Ting Wang, Sergio A. Rodriguez-Aponte, Christopher A. Naranjo, Justin Rhoades, Jesse D. Kirkpatrick, Heather E. Fleming, Ava P. Amini, Todd R. Golub, J. C. Love, Sangeeta N. Bhatia, V. Adalsteinsson
  
  Science | January 2024, 第 383 卷: pp. eadf2341-eadf2341
  
  DOI Publication
- Assessing the limits of zero-shot foundation models in single-cell biology
  
  Kasia Z. Kedzierska, Lorin Crawford, Ava P. Amini, Alex Lu
  
  bioRxiv | November 2023
  
  Preprint PDF 项目
- Continuous Time Evidential Distributions for Irregular Time Series
  
  Taylor W. Killian, Haoran Zhang, Thomas Hartvigsen, Ava P. Amini
  
  ArXiv | July 2023
  
  DOI Preprint
- Deep self-supervised learning for biosynthetic gene cluster detection and product classification
  
  Carolina Rios-Martinez, Nicholas Bhattacharya, Ava P. Amini, Lorin Crawford, Kevin Kaichuang Yang
  
  PLOS Computational Biology | May 2023, 第 19 卷(5)
  
  DOI Publication
- From noise to protein with image models
  
  Ava P. Amini, Kevin Kaichuang Yang
  
  Nature Computational Science | May 2023, 第 3 卷: pp. 366-367
  
  DOI Publication
- Low protease activity in B cell follicles promotes retention of intact antigens after immunization
  
  Aereas Aung, Ang Cui, Laura Maiorino, Ava P. Amini, Justin R. Gregory, Maurice Bukenya, Yiming Zhang, Heya Lee, Christopher A. Cottrell, Duncan M. Morgan, Murillo Silva, Heikyung Suh, Jesse D. Kirkpatrick, Parastoo Amlashi, Tanaka Remba, Leah M. Froehle, Shuhao Xiao, Wuhbet Abraham, Josetta Adams, J. Christopher Love, Phillip Huyett, Douglas S. Kwon, Nir Hacohen, William R. Schief, Sangeeta N. Bhatia, Darrell J. Irvine
  
  Science | January 2023, 第 379 卷(379): pp. eabn8934
  
  Publication
- A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
  
  Carmen Martin-Alonso, Shervin Tabrizi, Kan Xiong, Timothy Blewett, Sahil Patel, Zhenyi An, Sainetra Sridhar, Ahmet Bekdemir, Douglas Shea, Ava P. Amini, Shih-Ting Wang, Jesse Kirkpatrick, Justin Rhoades, Todd R. Golub, J. Christopher Love, Viktor A. Adalsteinsson, Sangeeta N. Bhatia
  
  bioRxiv | January 2023
  
  Preprint DOI
- Multiscale profiling of protease activity in cancer
  
  Ava P. Amini, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia
  
  Nature Communications | October 2022, 第 13 卷(1)
  
  Publication
- Protease activity analysis: A toolkit for analyzing enzyme activity data
  
  Ava P. Soleimany, Carmen Martin-Alonso, Melodi Anahtar, Cathy S. Wang, Sangeeta N. Bhatia
  
  ACS Omega | July 2022, 第 7 卷(28): pp. 24292-24301
  
  Publication
- Host protease activity classifies pneumonia etiology
  
  Melodi Anahtar, Leslie W. Chan, Henry Ko, Aditya Rao, Ava P. Soleimany, Purvesh Khatri, Sangeeta N. Bhatia
  
  Proceedings of the National Academy of Sciences of the United States of America | June 2022, 第 19 卷(25)
  
  Publication
- Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors
  
  Ahmet Bekdemir, Eden E. L. Tanner, Jesse Kirkpatrick, Ava P. Soleimany, Samir Mitragotri, Sangeeta N. Bhatia
  
  Advanced Healthcare Materials | February 2022, 第 11 卷(11)
  
  Publication
- Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection
  
  Jiang He, Lior Nissim, Ava P. Soleimany, Adina Binder-Nissim, Heather E. Fleming, Timothy K. Lu, Sangeeta N. Bhatia
  
  ACS Synthetic Biology | August 2021, 第 10 卷(9): pp. 2231-2242
  
  DOI Publication
- Evidential Deep Learning For Guided Molecular Property Prediction And Discovery
  
  Ava P. Soleimany, Alexander Amini, Samuel Goldman, Daniela Rus, Sangeeta N. Bhatia, Connor W. Coley
  
  ACS Central Science | July 2021, 第 7 卷(8): pp. 1356-1367
  
  Publication
- Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer
  
  Ava P. Soleimany, Jesse D. Kirkpatrick, Susan Su, Jaideep S. Dudani, Qian Zhong, Ahmet Bekdemir, Sangeeta N. Bhatia
  
  Cancer Research | January 2021, 第 81 卷(1): pp. 213-224
  
  DOI
- Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines
  
  Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine
  
  Nature Biomedical Engineering | May 2020, 第 4 卷(6): pp. 636-648
  
  DOI 项目
- Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring
  
  Ava P. Soleimany, Sangeeta N. Bhatia
  
  Trends in Molecular Medicine | April 2020, 第 26 卷(5): pp. 450-468
  
  DOI
- Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling
  
  Jesse D. Kirkpatrick, Andrew D. Warren, Ava P. Soleimany, Peter M. K. Westcott, Justin C. Voog, Carmen Martin-Alonso, Heather E. Fleming, Tuomas Tammela, Tyler Jacks, Sangeeta N. Bhatia
  
  Science Translational Medicine | March 2020, 第 12 卷(537)
  
  DOI
- Renal clearable catalytic gold nanoclusters for in vivo disease monitoring
  
  Colleen N. Loynachan, Ava P. Soleimany, Jaideep S. Dudani, Yiyang Lin, Adrian Najer, Ahmet Bekdemir, Qu Chen, Sangeeta N. Bhatia, Molly M. Stevens
  
  Nature Nanotechnology | August 2019, 第 14 卷(9): pp. 883-890
  
  DOI
- Synthetic recombinase-based state machines in living cells
  
  Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu
  
  Science | July 2016, 第 353 卷(6297): pp. 363-363
  
  DOI

Ava Amini

论文与出版物

scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Causal integration of chemical structures improves representations of microscopy images for morphological profiling

Toward deep learning sequence–structure co-generation for protein design

Deep learning guided design of protease substrates

Consequences of training data composition for deep learning models in single-cell biology

Benchmarking uncertainty quantification for protein engineering

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

Deeper evaluation of a single-cell foundation model

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Scalable, compressed phenotypic screening using pooled perturbations.

Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease

A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Protein structure generation via folding diffusion

Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies

Assessing the limits of zero-shot foundation models in single-cell biology

Continuous Time Evidential Distributions for Irregular Time Series

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

From noise to protein with image models

Low protease activity in B cell follicles promotes retention of intact antigens after immunization

A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies

Multiscale profiling of protease activity in cancer

Protease activity analysis: A toolkit for analyzing enzyme activity data

Host protease activity classifies pneumonia etiology

Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors

Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection

Evidential Deep Learning For Guided Molecular Property Prediction And Discovery

Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer

Deep Evidential Regression

Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines

Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring

Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling

Renal clearable catalytic gold nanoclusters for in vivo disease monitoring

Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure

Synthetic recombinase-based state machines in living cells

scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Causal integration of chemical structures improves representations of microscopy images for morphological profiling

Toward deep learning sequence–structure co-generation for protein design

Deep learning guided design of protease substrates

Consequences of training data composition for deep learning models in single-cell biology

Benchmarking uncertainty quantification for protein engineering

Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance

Deeper evaluation of a single-cell foundation model

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Scalable, compressed phenotypic screening using pooled perturbations.

Mutation and cell state compatibility is required and targetable in Ph+ acute lymphoblastic leukemia minimal residual disease

A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing

Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Protein structure generation via folding diffusion

Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

From noise to protein with image models

Low protease activity in B cell follicles promotes retention of intact antigens after immunization

A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies

Multiscale profiling of protease activity in cancer

Protease activity analysis: A toolkit for analyzing enzyme activity data

Host protease activity classifies pneumonia etiology

Ionic Liquid‐Mediated Transdermal Delivery of Thrombosis‐Detecting Nanosensors

Synthetic Circuit-Driven Expression of Heterologous Enzymes for Disease Detection

Activatable Zymography Probes Enable In Situ Localization of Protease Dysregulation in Cancer

Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines

Activity-Based Diagnostics: An Emerging Paradigm for Disease Detection and Monitoring

Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling

Renal clearable catalytic gold nanoclusters for in vivo disease monitoring

Uncovering and Mitigating Algorithmic Bias through Learned Latent Structure

Synthetic recombinase-based state machines in living cells

Causal integration of chemical structures improves representations of microscopy images for morphological profiling

Toward deep learning sequence–structure co-generation for protein design

Benchmarking uncertainty quantification for protein engineering

Protein generation with evolutionary diffusion: sequence is all you need

ProtNote: a multimodal method for protein-function annotation

Feature Reuse and Scaling: Understanding Transfer Learning with Protein Language Models

Protein structure generation via folding diffusion

Assessing the limits of zero-shot foundation models in single-cell biology

Continuous Time Evidential Distributions for Irregular Time Series